Mercurial > repos > jay > pdaug_basic_plots
diff PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 4:080b372fe513 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author | jay |
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date | Tue, 12 Jan 2021 18:47:41 +0000 |
parents | 65c196b084ff |
children |
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--- a/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Wed Dec 30 02:47:51 2020 +0000 +++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Tue Jan 12 18:47:41 2021 +0000 @@ -1,64 +1,72 @@ -import os -import argparse + +import pandas as pd + + +def TSVtoFASTA(infile, method, firstdatafile, seconddatafile, outfile, clmpepid, slcclasslabel, peps): + + + fn = [firstdatafile, seconddatafile] -def TSVtoFASTA(InFile, Method, Positive, Negative, OutFile): - - if Method == 'WithClassLabel': - - f = open(InFile) - lines = f.readlines() - - of1 = open(Positive,'w') - of2 = open(Negative,'w') - - n = 0 - m = 0 - - l = [] - - for line in lines[1:]: - l.append(line.split('\t')[1].strip('\n').strip('\r')) - l = list(set(l)) - - print(l) - - for line in lines: + df = pd.read_csv(infile, sep="\t") + if clmpepid == None: + pass + else: + names = df[clmpepid].tolist() - if l[1] in line.split('\t')[1].strip('\n').strip('\r'): - n= n+1 - of1.write('>peptide_'+str(n)+'_'+str(l[1])+'\n') - of1.write(line.split('\t')[0]+'\n') - - if l[0] in line.split('\t')[1].strip('\n').strip('\r'): - m= m+1 - of2.write('>peptide_'+str(m)+'_'+str(l[0])+'\n') - of2.write(line.split('\t')[0]+'\n') + peps = df[peps].tolist() + + if method == "withoutlabel": + f = open(outfile,'w') + if clmpepid is not None: + for i,n in enumerate(peps): + f.write(">"+names[i]+'\n') + f.write(n+'\n') + f.close() + else: + for i,n in enumerate(peps): + f.write(">"+str(i)+'\n') + f.write(n+'\n') + f.close() + + elif method == "withlabel": + labels = df[slcclasslabel].tolist() - elif Method == 'NoClassLabel': - - f = open(InFile) - lines = f.readlines() - of1 = open(OutFile,'w') - - for i, line in enumerate(lines[1:]): - of1.write('>peptide_'+str(i)+'\n') - of1.write(line.split('\t')[0]+'\n') - - else: - pass + label = list(set(labels)) + + if clmpepid is None: + for i, l in enumerate(label): + f = open(fn[i],'w') + print('ok1') + for i, L in enumerate(labels): + if l == L: + f.write(">"+str(i)+"_"+str(l)+'\n') + f.write(peps[i]+'\n') + f.close() + else: + for i, l in enumerate(label): + f = open(fn[i],'w') + for i, L in enumerate(labels): + if l == L: + f.write(">"+names[i]+"_"+l+'\n') + f.write(peps[i]+'\n') + f.close() if __name__=="__main__": import argparse - parser = argparse.ArgumentParser() - parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv") - parser.add_argument("-P", "--Postvs", required=False, default='FirstDataFile.fasta', help="Path to target tsv file") - parser.add_argument("-N", "--Negtvs", required=False, default='SecondDataFile.fasta', help="Path to target tsv file") + parser.add_argument("-F", "--FirstDataFile", required=False, default='FirstDataFile.fasta', help="Path to target tsv file") + parser.add_argument("-S", "--SecondDataFile", required=False, default='SecondDataFile.fasta', help="Path to target tsv file") parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file") parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file") + parser.add_argument("-C", "--ClmPepID", required=False, default=None, help="Peptide Column Name") + parser.add_argument("-L", "--SlcClassLabel", required=False, default="Class_label", help="Class Label Column Name") + parser.add_argument("-P", "--PeptideColumn", required=True, default=None, help="Class Label Column Name") args = parser.parse_args() - TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile) \ No newline at end of file + TSVtoFASTA(args.InFile, args.Method, args.FirstDataFile, args.SecondDataFile, args.OutFile, args.ClmPepID, args.SlcClassLabel, args.PeptideColumn) + + +